Remove Tracking Markers
Removing the markers is quite simple:

What you need:


Scale accurate model of the mini-figures head
A million dollars and contacts at ILM :P


What you need to do


Align your model of the mini figure to the tracked head exactly even the slightest error can be catastrophic. 
Project the image back onto the model head, using the UV project modifier. Be sure the create a UV map specifically for this purpose. It doesn't matter what it looks like since it will be overwritten. See image for settings.
Create a B&amp;W matte on the model head, using texture paint, of where you wan't to remove the markers. Be sure to feather it. You may wan't to create a matte for each and every marker (see later steps), but it will be a pain.
Take your projected image, and move it up or down based on where available matching pixels are. You may need to do this on an individual marker bases. The example material only supports one direction.
Make the texture shadless (BTW, because of the complex mapping, I'd this in cycles, it will render pretty fast since it will only be an emission shader) be sure to make it transparent outside of the white areas of your matte.



Click for larger image


Render and composite over!
If it doesn't work, kiss your million bye bye and call up your buddies at ILM!


Final notes: 


For best results you should update the texture on each frame, so that the paint over will animate with the reflections, which is why I recommended the UV project modifier.
If you have trouble, just ask which steps you need elaborated.
This will take some tweaking to make it look correct.